shnitsel._generated_accessors

Classes

DataArrayAccessor
DatasetAccessor

Module Contents

class DataArrayAccessor(obj)

Bases: shnitsel._accessors.DAManualAccessor

_methods = ['norm', 'subtract_combinations', 'keep_norming', 'pwdists', 'calc_confidence_interval',...

norm(dim='direction', keep_attrs=None)

Wrapper for shnitsel.analyze.generic.norm().

Parameters:

• dim (Hashable)

• keep_attrs (bool | str | None)

Return type:

xarray.core.dataarray.DataArray

subtract_combinations(dim, labels=False)

Wrapper for shnitsel.analyze.generic.subtract_combinations().

Parameters:

• dim (Hashable)

• labels (bool)

Return type:

xarray.core.dataarray.DataArray

keep_norming(exclude=None)

Wrapper for shnitsel.analyze.generic.keep_norming().

Parameters:

exclude (Optional)

Return type:

xarray.core.dataarray.DataArray

pwdists(mean=False)

Wrapper for shnitsel.analyze.generic.pwdists().

Parameters:

mean (bool)

Return type:

xarray.core.dataarray.DataArray

calc_confidence_interval(confidence=0.95)

Wrapper for shnitsel.analyze.stats.calc_confidence_interval().

Parameters:

confidence (float)

Return type:

numpy.ndarray

time_grouped_confidence_interval(confidence=0.9)

Wrapper for shnitsel.analyze.stats.time_grouped_confidence_interval().

Parameters:

confidence (float)

Return type:

xarray.core.dataset.Dataset

to_xyz(comment='#', units='angstrom')

Wrapper for shnitsel.bridges.to_xyz().

Return type:

str

traj_to_xyz(units='angstrom')

Wrapper for shnitsel.bridges.traj_to_xyz().

Return type:

str

to_mol(charge=None, covFactor=1.2, to2D=True, molAtomMapNumber=None, atomNote=None, atomLabel=None)

Wrapper for shnitsel.bridges.to_mol().

Parameters:

• charge (int | None)

• covFactor (float)

• to2D (bool)

• molAtomMapNumber (Union)

• atomNote (Union)

• atomLabel (Union)

Return type:

rdkit.Chem.rdchem.Mol

smiles_map(charge=0, covFactor=1.5)

Wrapper for shnitsel.bridges.smiles_map().

Return type:

str

default_mol()

Wrapper for shnitsel.bridges.default_mol().

Return type:

rdkit.Chem.rdchem.Mol

pairwise_dists_pca(mean=False, return_pca_object=False, **kwargs)

Wrapper for shnitsel.analyze.pca.pairwise_dists_pca().

Parameters:

mean (bool)

Return type:

xarray.core.dataarray.DataArray

convert_energy(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_energy().

Parameters:

• to (str)

• convert_from (str | None)

convert_force(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_force().

Parameters:

• to (str)

• convert_from (str | None)

convert_dipole(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_dipole().

Parameters:

• to (str)

• convert_from (str | None)

convert_length(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_length().

Parameters:

• to (str)

• convert_from (str | None)

convert_time(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_time().

Parameters:

• to (str)

• convert_from (str | None)

convert_nacs(to, convert_from=None)

Wrapper for shnitsel.units.conversion.convert_nacs().

Parameters:

• to (str)

• convert_from (str | None)

mdiff()

Wrapper for shnitsel.data.multi_indices.mdiff().

Return type:

xarray.DataArray

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)

Wrapper for shnitsel.data.multi_indices.flatten_levels().

Parameters:

• idx_name (str)

• levels (Sequence[str])

• new_name (str | None)

• position (int)

• renamer (Callable | None)

Return type:

shnitsel.core.typedefs.DatasetOrArray

expand_midx(midx_name, level_name, value)

Wrapper for shnitsel.data.multi_indices.expand_midx().

Parameters:

• midx_name (str)

• level_name (str)

Return type:

shnitsel.core.typedefs.DatasetOrArray

assign_levels(levels=None, **levels_kwargs)

Wrapper for shnitsel.data.multi_indices.assign_levels().

Parameters:

• levels (dict[str, numpy.typing.ArrayLike] | None)

• levels_kwargs (numpy.typing.ArrayLike)

Return type:

shnitsel.core.typedefs.DatasetOrArray

mgroupby(levels)

Wrapper for shnitsel.data.multi_indices.mgroupby().

Parameters:

levels (Sequence[str])

Return type:

xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)

Wrapper for shnitsel.data.multi_indices.msel().

Return type:

xarray.Dataset | xarray.DataArray

sel_trajs(trajids_or_mask, invert=False)

Wrapper for shnitsel.data.multi_indices.sel_trajs().

Parameters:

trajids_or_mask (Sequence[int] | Sequence[bool])

Return type:

xarray.Dataset | xarray.DataArray

sel_trajids(trajids, invert=False)

Wrapper for shnitsel.data.multi_indices.sel_trajids().

Parameters:

trajids (numpy.typing.ArrayLike)

Return type:

xarray.Dataset

true_upto(dim)

Wrapper for shnitsel.clean.common.true_upto().

dihedral(i, j, k, l, deg=False, full=False)

Wrapper for shnitsel.geo.geocalc.dihedral().

Parameters:

• i (int)

• j (int)

• k (int)

• l (int)

• deg (bool)

• full (bool)

Return type:

xarray.core.dataarray.DataArray

angle(i, j, k, deg=False)

Wrapper for shnitsel.geo.geocalc.angle().

Parameters:

• i (int)

• j (int)

• k (int)

• deg (bool)

Return type:

xarray.core.dataarray.DataArray

distance(i, j)

Wrapper for shnitsel.geo.geocalc.distance().

Parameters:

• i (int)

• j (int)

Return type:

xarray.core.dataarray.DataArray

get_bond_lengths(matches_or_mol=None)

Wrapper for shnitsel.geo.geocalc.get_bond_lengths().

Parameters:

matches_or_mol (dict | rdkit.Chem.rdchem.Mol | None)

Return type:

xarray.core.dataarray.DataArray

get_bond_angles(matches_or_mol=None, mol=None, ang=False)

Wrapper for shnitsel.geo.geocalc.get_bond_angles().

Parameters:

• matches_or_mol (dict | rdkit.Chem.rdchem.Mol | None)

• mol (rdkit.Chem.rdchem.Mol | None)

• ang (Literal)

Return type:

xarray.core.dataarray.DataArray

get_bond_torsions(matches_or_mol=None, signed=None, ang=False)

Wrapper for shnitsel.geo.geocalc.get_bond_torsions().

Parameters:

• matches_or_mol (dict | None)

• signed (bool | None)

• ang (Literal)

Return type:

xarray.core.dataarray.DataArray

get_pyramids(pyramid_idxs=None, mol=None, deg=False, signed=True)

Wrapper for shnitsel.geo.geocalc.get_pyramids().

Parameters:

• pyramid_idxs (dict[int, list[int]] | None)

• mol (rdkit.Chem.rdchem.Mol | None)

• deg (bool)

Return type:

xarray.core.dataarray.DataArray

get_bats(matches_or_mol=None, signed=None, ang=False, pyr=False)

Wrapper for shnitsel.geo.geocalc.get_bats().

Parameters:

• matches_or_mol (dict | rdkit.Chem.rdchem.Mol | None)

• signed (bool | None)

• ang (Literal)

Return type:

xarray.core.dataarray.DataArray

kabsch(reference_or_indexers=None, **indexers_kwargs)

Wrapper for shnitsel.geo.geocalc.kabsch().

Parameters:

reference_or_indexers (xarray.core.dataarray.DataArray | dict | None)

Return type:

xarray.core.dataarray.DataArray

FrameSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.FrameSelector().

TrajSelector(xname=None, yname=None, title='', allowed_ws_origin=None, webgl=True)

Wrapper for shnitsel.vis.plot.select.TrajSelector().

frame3D()

Wrapper for shnitsel.vis.plot.p3mhelpers.frame3D().

frames3Dgrid()

Wrapper for shnitsel.vis.plot.p3mhelpers.frames3Dgrid().

traj3D()

Wrapper for shnitsel.vis.plot.p3mhelpers.traj3D().

trajs3Dgrid(trajids=None, loop='forward')

Wrapper for shnitsel.vis.plot.p3mhelpers.trajs3Dgrid().

Parameters:

trajids (list[int | str] | None)

traj_vmd(groupby='trajid')

Wrapper for shnitsel.vis.vmd.traj_vmd().

pca(dim, n_components=2, return_pca_object=False)

Wrapper for shnitsel.analyze.pca.pca().

Parameters:

• dim (str)

• n_components (int)

• return_pca_object (bool)

Return type:

tuple[xarray.core.dataarray.DataArray, sklearn.decomposition._pca.PCA] | xarray.core.dataarray.DataArray

lda(dim, cats, n_components=2)

Wrapper for shnitsel.analyze.lda.lda().

Parameters:

• dim (str)

• cats (str | xarray.core.dataarray.DataArray)

• n_components (int)

Return type:

xarray.core.dataarray.DataArray

pls(ydata_array, n_components=2, common_dim=None)

Wrapper for shnitsel.analyze.pls.pls().

Parameters:

• ydata_array (xarray.core.dataarray.DataArray)

• n_components (int)

• common_dim (str | None)

Return type:

xarray.core.dataset.Dataset

class DatasetAccessor(obj)

Bases: shnitsel._accessors.DSManualAccessor

_methods = ['pca_and_hops', 'validate', 'assign_fosc', 'ds_broaden_gauss', 'get_per_state',...

pca_and_hops(mean)

Wrapper for shnitsel.analyze.pca.pca_and_hops().

Parameters:

mean (bool)

Return type:

tuple

validate()

Wrapper for shnitsel.data.helpers.validate().

Return type:

numpy.ndarray

assign_fosc()

Wrapper for shnitsel.analyze.spectra.assign_fosc().

Return type:

xarray.core.dataset.Dataset

ds_broaden_gauss(width_in_eV=0.5, nsamples=1000, xmax=None)

Wrapper for shnitsel.analyze.spectra.ds_broaden_gauss().

Parameters:

• width_in_eV (float)

• nsamples (int)

• xmax (float | None)

Return type:

xarray.core.dataarray.DataArray

get_per_state()

Wrapper for shnitsel.analyze.stats.get_per_state().

Return type:

xarray.core.dataset.Dataset

get_inter_state()

Wrapper for shnitsel.analyze.stats.get_inter_state().

Return type:

xarray.core.dataset.Dataset

calc_classical_populations()

Wrapper for shnitsel.analyze.populations.calc_classical_populations().

Return type:

xarray.core.dataarray.DataArray

default_mol()

Wrapper for shnitsel.bridges.default_mol().

Return type:

rdkit.Chem.rdchem.Mol

flatten_levels(idx_name, levels, new_name=None, position=0, renamer=None)

Wrapper for shnitsel.data.multi_indices.flatten_levels().

Parameters:

• idx_name (str)

• levels (Sequence[str])

• new_name (str | None)

• position (int)

• renamer (Callable | None)

Return type:

shnitsel.core.typedefs.DatasetOrArray

expand_midx(midx_name, level_name, value)

Wrapper for shnitsel.data.multi_indices.expand_midx().

Parameters:

• midx_name (str)

• level_name (str)

Return type:

shnitsel.core.typedefs.DatasetOrArray

assign_levels(levels=None, **levels_kwargs)

Wrapper for shnitsel.data.multi_indices.assign_levels().

Parameters:

• levels (dict[str, numpy.typing.ArrayLike] | None)

• levels_kwargs (numpy.typing.ArrayLike)

Return type:

shnitsel.core.typedefs.DatasetOrArray

mgroupby(levels)

Wrapper for shnitsel.data.multi_indices.mgroupby().

Parameters:

levels (Sequence[str])

Return type:

xarray.core.groupby.DataArrayGroupBy | xarray.core.groupby.DatasetGroupBy

msel(**kwargs)

Wrapper for shnitsel.data.multi_indices.msel().

Return type:

xarray.Dataset | xarray.DataArray

sel_trajs(trajids_or_mask, invert=False)

Wrapper for shnitsel.data.multi_indices.sel_trajs().

Parameters:

trajids_or_mask (Sequence[int] | Sequence[bool])

Return type:

xarray.Dataset | xarray.DataArray

unstack_trajs()

Wrapper for shnitsel.data.multi_indices.unstack_trajs().

Return type:

shnitsel.core.typedefs.DatasetOrArray

stack_trajs()

Wrapper for shnitsel.data.multi_indices.stack_trajs().

Return type:

xarray.Dataset | xarray.DataArray

write_shnitsel_file(savepath, complevel=9)

Wrapper for shnitsel.io.shnitsel.write.write_shnitsel_file().

Parameters:

• savepath (str | os.PathLike)

• complevel (int)

spectra_all_times()

Wrapper for shnitsel.analyze.spectra.spectra_all_times().

Return type:

xarray.core.dataarray.DataArray

energy_filtranda(etot_drift=None, etot_step=None, epot_step=None, ekin_step=None, hop_epot_step=None, units='eV')

Wrapper for shnitsel.clean.filter_energy.energy_filtranda().

Parameters:

• etot_drift (float | None)

• etot_step (float | None)

• epot_step (float | None)

• ekin_step (float | None)

• hop_epot_step (float | None)

sanity_check(cut='truncate', units='eV', etot_drift=nan, etot_step=nan, epot_step=nan, ekin_step=nan, hop_epot_step=nan, plot_thresholds=False, plot_populations=False)

Wrapper for shnitsel.clean.filter_energy.sanity_check().

Parameters:

• cut (Union)

• etot_drift (float)

• etot_step (float)

• epot_step (float)

• ekin_step (float)

• hop_epot_step (float)

• plot_thresholds (Union)

• plot_populations (Union)

bond_length_filtranda(search_dict=None, units='angstrom', mol=None)

Wrapper for shnitsel.clean.filter_geo.bond_length_filtranda().

Parameters:

• search_dict (dict[str, numbers.Number] | None)

• mol (rdkit.Chem.rdchem.Mol | None)

filter_by_length(cut='truncate', search_dict=None, units='angstrom', plot_thresholds=False, plot_populations=False, mol=None)

Wrapper for shnitsel.clean.filter_geo.filter_by_length().

Parameters:

• cut (Union)

• search_dict (dict[str, numbers.Number] | None)

• units (str)

• plot_thresholds (Union)

• plot_populations (Union)

• mol (rdkit.Chem.rdchem.Mol | None)

omit()

Wrapper for shnitsel.clean.common.omit().

truncate()

Wrapper for shnitsel.clean.common.truncate().

transect(cutoff)

Wrapper for shnitsel.clean.common.transect().

Parameters:

cutoff (float)

write_ase_db(db_path, db_format, keys_to_write=None, preprocess=True)

Wrapper for shnitsel.io.ase.write.write_ase_db().

Parameters:

• db_path (str)

• db_format (Optional)

• keys_to_write (Optional)

• preprocess (bool)

pls_ds(xname, yname, n_components=2, common_dim=None)

Wrapper for shnitsel.analyze.pls.pls_ds().

Parameters:

• xname (str)

• yname (str)

• n_components (int)

• common_dim (str | None)

Return type:

xarray.core.dataset.Dataset